There has never been a more exciting time to be at the interface of biological engineering and petroleum geosciences. Recent discoveries in geomicrobiology and methodological breakthroughs in DNA sequencing place us on the brink of an unprecedented understanding of the role of microorganisms in globally significant processes in subsurface petroleum reservoirs. Qualified estimates reveal that the vast majority of microorganisms on Earth inhabit the subsurface. Most newly discovered taxa in this 'deep biosphere' have no representatives in laboratory cultures, thus knowledge about their role in economically relevant biogeochemical cycles is unknown. Fossil fuel reservoirs are microbial habitats of great scientific interest and even greater societal importance. Microbes native to subsurface petroleum reservoirs can cause significant damage and economic loss. However, understanding and harnessing this 'petroleum microbiome' has great potential for engineering interventions for more sustainable petroleum production and novel exploration strategies.The next generation of engineers faces the unavoidable challenge of reducing global greenhouse gas emissions. The oil and gas industry is at the epicentre of this challenge. Currently fossil fuels account for greater than 80% of global primary energy supply, yet even under optimistic projections of rapid innovation and modest population growth fossil fuels will still supply 70% of our energy in 2030 (International Energy Agency, 2010). It is clear that the transition towards more sustainable energy will require several decades, that fossil fuels will continue to be essential, and that innovation is needed in all areas of the energy sector. It is critical therefore to develop new engineering interventions and novel technologies focusing directly on the oil indsutry so that existing resources are exploited as responsibly as possible.It has long been recognized that microorganisms are important constituents of petroleum reservoirs and oil production systems, with the presence of sulfate-reducing bacteria (SRB) being reported almost a century ago (Bastin, 1926, Science 63:21). SRB are well known in the oil industry because they cause reservoir souring - the production of toxic hydrogen sulfide (H2S). Souring costs the oil industry billions of pounds annually due to production problems related to H2S (e.g., corrosion) and the lower value of high-sulfur petroleum. Nitrate-reducing bacteria (NRB) can be stimulated to control souring in an environmentally friendly way, and while nitrate injection is a strategy beginning to be practised offshore, it remains poorly understood. The first major objective of DEEPBIOENGINEERING is to develop a new understanding of souring and nitrate-driven souring control by applying a combination of geochemistry, microbiology and high throughput nucleic acid sequencing to reservoir production waters and experimental cultures inoculated with them. This research will deliver an unprecedented understanding of the petroleum microbiome, which will underpin prediction-based bioengineering interventions for souring control.The second major objective of DEEPBIOENGINEERING is to exploit the knowledge of the deep petroleum microbiome to track the distribution of formerly indigenous reservoir bacteria. This will lead to a totally new tool for offshore oil and gas exploration. This idea is based on the observation of oil reservoir-like bacteria (thermophilic SRB) in cold ocean sediments (Hubert et al 2009, Science 325:1541) and the hypothesis that petroleum fluids leaking from reservoirs at natural seafloor hydrocarbon seeps is a mechanism for microbe dispersal that can be quantitatively measured. This will lead to predictive models and concepts that will be use bioindicators to map the seafloor and predict or locate seabed hydrocarbon seeps. This environmentally friendly tool will assist offshore exploration for needed petroleum energy resources.

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